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How do shotgun proteomics algorithms identify proteins?

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Instrumentation aside, algorithms for matching mass spectra to proteins are at the heart of shotgun proteomics. How do these algorithms work, what can we expect of them and why is it so difficult to find protein modifications?

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Figure 1: Shotgun proteomics identifies proteins from the fragmentation mass spectra of their constituent peptides.

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Authors and Affiliations

  1. Edward Marcotte is at the Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, MBB 3.210, Austin, Texas, 78712, USA. marcotte@icmb.utexas.edu,

    Edward M Marcotte

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  1. Edward M Marcotte
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Marcotte, E. How do shotgun proteomics algorithms identify proteins?. Nat Biotechnol 25, 755–757 (2007). https://doi.org/10.1038/nbt0707-755

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